Rarefaction curves of all sites for MiFish amplicon

1 Argentina

iNEXT_data_Arg <- readRDS("iNEXT_data_Arg.rds")

palette <- c("gray34","#4e693a","#88b564","#4e693a","#4e693a","#4e693a","#9bcf72",
             "#749b55","#9bcf72","#749b55","#749b55","#749b55","#9bcf72",
             "#ade880","gray34","#88b564","#ade880","#88b564","#88b564",
             "#9bcf72","#ade880","#ade880")

# Sample-size-based rarefaction/extrapolation curve
suppressMessages({ 
  p1 <- ggiNEXT(iNEXT_data_Arg, type=1, color.var = "Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
}) 

# Sample completeness curve
suppressMessages({ 
  p2 <- ggiNEXT(iNEXT_data_Arg, type=2, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
}) 

# Coverage-based rarefaction/extrapolation curve
suppressMessages({ 
  p3 <- ggiNEXT(iNEXT_data_Arg, type=3, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
}) 

suppressMessages({ 
  suppressWarnings({ 
ggarrange(p1, p2, p3 + rremove("x.text"), 
          labels = c("A", "B", "C"),
          ncol = 2, nrow = 2, common.legend = T, legend = "right")
  })
})

2 Bangladesh

iNEXT_data_Ban <- readRDS("iNEXT_data_Ban.rds")

palette <- c("grey34","#2d573c","#53a36f","#67c989","#193021","#2d573c",
             "#2d573c","#53a36f","#53a36f","#7af0a3","#67c989","#7af0a3",
             "#7af0a3","#407d55","#2d573c","#67c989","#67c989","#407d55",
             "#407d55","#407d55","#7af0a3","#53a36f")

# Sample-size-based rarefaction/extrapolation curve
suppressMessages({
  p1 <- ggiNEXT(iNEXT_data_Ban, type=1, color.var = "Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
  }) 

# Sample completeness curve
suppressMessages({
  p2 <- ggiNEXT(iNEXT_data_Ban, type=2, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
  }) 

# Coverage-based rarefaction/extrapolation curve
suppressMessages({
  p3 <- ggiNEXT(iNEXT_data_Ban, type=3, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
  }) 

suppressMessages({
  suppressWarnings({
    ggarrange(p1, p2, p3 + rremove("x.text"), 
          labels = c("A", "B", "C"),
          ncol = 2, nrow = 2, common.legend = T, legend = "right")
    })
  })

3 Belize

iNEXT_data_Bel <- readRDS("iNEXT_data_Bel.rds")

palette <- c("grey34","#21203b","#625ead","#4c4987","#4c4987","#625ead",
             "#21203b","#625ead","#373461","#625ead","#7570d1","#373461",
             "#373461","#4c4987","#21203b","#4c4987","#21203b","#373461")

# Sample-size-based rarefaction/extrapolation curve
suppressMessages({
  p1 <- ggiNEXT(iNEXT_data_Bel, type=1, color.var = "Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
  }) 

# Sample completeness curve
suppressMessages({  
  p2 <- ggiNEXT(iNEXT_data_Bel, type=2, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
  }) 

# Coverage-based rarefaction/extrapolation curve
suppressMessages({  p3 <- ggiNEXT(iNEXT_data_Bel, type=3, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
}) 

suppressMessages({
  suppressWarnings({
    ggarrange(p1, p2, p3 + rremove("x.text"), 
          labels = c("A", "B", "C"),
          ncol = 2, nrow = 2, common.legend = T, legend = "right")
    })
  })

4 Brazil

iNEXT_data_Bra <- readRDS("iNEXT_data_Bra.rds")

palette <- c("gray34","#454215","#787424","#aba433","#aba433","#454215","#aba433",
             "gray34","#787424","#787424","#aba433","#454215","#454215",
             "#787424")

# Sample-size-based rarefaction/extrapolation curve
suppressMessages({
  p1 <- ggiNEXT(iNEXT_data_Bra, type=1, color.var = "Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
  }) 

# Sample completeness curve
suppressMessages({  p2 <- ggiNEXT(iNEXT_data_Bra, type=2, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
}) 

# Coverage-based rarefaction/extrapolation curve
suppressMessages({  p3 <- ggiNEXT(iNEXT_data_Bra, type=3, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
}) 

suppressMessages({
  suppressWarnings({
    ggarrange(p1, p2, p3 + rremove("x.text"), 
          labels = c("A", "B", "C"),
          ncol = 2, nrow = 2, common.legend = T, legend = "right")
    })
  })

5 CocosIsland

iNEXT_data_Coco <- readRDS("iNEXT_data_Coco.rds")

palette <- c("gray34","#1e111f","#9c5a9e","#b669b8","#b669b8","#834c85",
             "#e786eb","#9c5a9e","#ce77d1","#9c5a9e","#e786eb","#1e111f",
             "#b669b8","#9c5a9e","#b669b8","#e786eb","#834c85","#1e111f",
             "#834c85","#834c85","#e786eb","#1e111f","#ce77d1","#ce77d1",
             "#ce77d1","#ce77d1")

# Sample-size-based rarefaction/extrapolation curve
suppressMessages({  p1 <- ggiNEXT(iNEXT_data_Coco, type=1, color.var = "Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
}) 

# Sample completeness curve
suppressMessages({  p2 <- ggiNEXT(iNEXT_data_Coco, type=2, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
}) 

# Coverage-based rarefaction/extrapolation curve
suppressMessages({  p3 <- ggiNEXT(iNEXT_data_Coco, type=3, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
}) 


suppressMessages({
  suppressWarnings({
    ggarrange(p1, p2, p3 + rremove("x.text"), 
          labels = c("A", "B", "C"),
          ncol = 2, nrow = 2, common.legend = T, legend = "right")
    })
  })

6 Coiba

iNEXT_data_Coi <- readRDS("iNEXT_data_Coi.rds")

palette <- c("#5bf9fc","#246263","#3fadaf","#3fadaf","#246263","#32888a",
             "#5bf9fc","#163d3d","#32888a","#246263","#4dd4d6","#246263",
             "#5bf9fc","#3fadaf","#4dd4d6","#3fadaf","#4dd4d6","#4dd4d6",
             "#5bf9fc","#32888a","#32888a","gray34")

# Sample-size-based rarefaction/extrapolation curve
suppressMessages({
  p1 <- ggiNEXT(iNEXT_data_Coi, type=1, color.var = "Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
}) 

# Sample completeness curve
suppressMessages({
  p2 <- ggiNEXT(iNEXT_data_Coi, type=2, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
  }) 

# Coverage-based rarefaction/extrapolation curve
suppressMessages({
  p3 <- ggiNEXT(iNEXT_data_Coi, type=3, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
  }) 

suppressMessages({  
  suppressWarnings({
    ggarrange(p1, p2, p3 + rremove("x.text"), 
          labels = c("A", "B", "C"),
          ncol = 2, nrow = 2, common.legend = T, legend = "right")
    })
  })

7 Everglades

iNEXT_data_Eve <- readRDS("iNEXT_data_Eve.rds")

palette <- c("#ed7351","#54291d","#a14e37","#c86145","#c86145","#ed7351",
             "#ed7351","#7a3b2a","#54291d","#54291d","#54291d","#c86145",
             "#7a3b2a","#7a3b2a","#7a3b2a","#c86145","#ed7351","#7a3b2a",
             "#a14e37","#a14e37","#a14e37","gray34","gray34")

# Sample-size-based rarefaction/extrapolation curve
suppressMessages({
  p1 <- ggiNEXT(iNEXT_data_Eve, type=1, color.var = "Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
  }) 

# Sample completeness curve
suppressMessages({
  p2 <- ggiNEXT(iNEXT_data_Eve, type=2, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
  }) 

# Coverage-based rarefaction/extrapolation curve
suppressMessages({
  p3 <- ggiNEXT(iNEXT_data_Eve, type=3, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
  }) 

suppressMessages({  
  suppressWarnings({
    ggarrange(p1, p2, p3 + rremove("x.text"), 
          labels = c("A", "B", "C"),
          ncol = 2, nrow = 2, common.legend = T, legend = "right")
    })
  })

8 LordHowe

iNEXT_data_Lor <- readRDS("iNEXT_data_Lor.rds")

palette <- c("#542636","#c75980","#c75980","#c75980","#7a374f","#7a374f",
             "#ed6b98","gray34","#542636","#a14867","#a14867","#ed6b98",
             "#a14867","#a14867","#542636","#7a374f","#7a374f","#c75980",
             "#ed6b98","#ed6b98","#542636","gray34")

# Sample-size-based rarefaction/extrapolation curve
suppressMessages({
  p1 <- ggiNEXT(iNEXT_data_Lor, type=1, color.var = "Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
  }) 

# Sample completeness curve
suppressMessages({
  p2 <- ggiNEXT(iNEXT_data_Lor, type=2, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
  }) 

# Coverage-based rarefaction/extrapolation curve
suppressMessages({
  p3 <- ggiNEXT(iNEXT_data_Lor, type=3, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
  }) 

suppressMessages({  
  suppressWarnings({
    ggarrange(p1, p2, p3 + rremove("x.text"), 
          labels = c("A", "B", "C"),
          ncol = 2, nrow = 2, common.legend = T, legend = "right")
    })
  })

9 Mauritania

iNEXT_data_Mau <- readRDS("iNEXT_data_Mau.rds")

palette <- c("#cf832d","#cf832d","#cf832d","#cf832d","#cf832d","#cf832d",
             "#cf832d","#cf832d","#cf832d","#cf832d","#cf832d","#cf832d",
             "#cf832d","#cf832d","#cf832d","#cf832d","#cf832d","#cf832d",
             "#cf832d","#cf832d","#cf832d","gray34")

# Sample-size-based rarefaction/extrapolation curve
suppressMessages({
  p1 <- ggiNEXT(iNEXT_data_Mau, type=1, color.var = "Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
  }) 

# Sample completeness curve
suppressMessages({
  p2 <- ggiNEXT(iNEXT_data_Mau, type=2, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
  }) 

# Coverage-based rarefaction/extrapolation curve
suppressMessages({
  p3 <- ggiNEXT(iNEXT_data_Mau, type=3, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
  }) 

suppressMessages({    
  suppressWarnings({  
    ggarrange(p1, p2, p3 + rremove("x.text"), 
          labels = c("A", "B", "C"),
          ncol = 2, nrow = 2, common.legend = T, legend = "right")
    })
  })

10 Mexico

iNEXT_data_Mex <- readRDS("iNEXT_data_Mex.rds")

palette <- c("#698fca","#698fca","#344763","#83b3fc","#83b3fc","#4e6b96",
             "#83b3fc","#698fca","#4e6b96","#83b3fc","#83b3fc","gray34",
             "#344763","#698fca","#344763","#83b3fc","#83b3fc","#4e6b96",
             "#83b3fc","#344763","#4e6b96","gray34")

# Sample-size-based rarefaction/extrapolation curve
suppressMessages({
  p1 <- ggiNEXT(iNEXT_data_Mex, type=1, color.var = "Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
  }) 

# Sample completeness curve
suppressMessages({
  p2 <- ggiNEXT(iNEXT_data_Mex, type=2, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
  }) 

# Coverage-based rarefaction/extrapolation curve
suppressMessages({
  p3 <- ggiNEXT(iNEXT_data_Mex, type=3, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
  }) 

suppressMessages({    
  suppressWarnings({  
    ggarrange(p1, p2, p3 + rremove("x.text"), 
          labels = c("A", "B", "C"),
          ncol = 2, nrow = 2, common.legend = T, legend = "right")
    })
  })

11 NewCaledonia

iNEXT_data_New <- readRDS("iNEXT_data_New.rds")

palette <- c("#d4fa4b","#52611d","#b4d43f","#52611d","#94ae35","#738729",
             "#738729","#52611d","#d4fa4b","#94ae35","#b4d43f","#d4fa4b",
             "#94ae35","#738729","#52611d","#738729","#b4d43f","#94ae35",
             "#d4fa4b","gray34")

# Sample-size-based rarefaction/extrapolation curve
suppressMessages({
  p1 <- ggiNEXT(iNEXT_data_New, type=1, color.var = "Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette)
  }) 

# Sample completeness curve
suppressMessages({  
  p2 <- ggiNEXT(iNEXT_data_New, type=2, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

# Coverage-based rarefaction/extrapolation curve
suppressMessages({  
  p3 <- ggiNEXT(iNEXT_data_New, type=3, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

suppressMessages({    
  suppressWarnings({  
    ggarrange(p1, p2, p3 + rremove("x.text"), 
          labels = c("A", "B", "C"),
          ncol = 2, nrow = 2, common.legend = T, legend = "right")
    }) 
  })

12 Ningaloo

iNEXT_data_Nin <- readRDS("iNEXT_data_Nin.rds")

palette <- c("#9f6cbd","#7f5696","#7f5696","#3f2a4a","gray34","#9f6cbd",
             "#3f2a4a","#bf81e3","#3f2a4a","#3f2a4a","#bf81e3","#9f6cbd",
             "#bf81e3","#7f5696","#3f2a4a","#9f6cbd","#5f4070","#5f4070",
             "#5f4070","#7f5696","#bf81e3","gray34")

# Sample-size-based rarefaction/extrapolation curve
suppressMessages({  
  p1 <- ggiNEXT(iNEXT_data_Nin, type=1, color.var = "Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

# Sample completeness curve
suppressMessages({  
  p2 <- ggiNEXT(iNEXT_data_Nin, type=2, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

# Coverage-based rarefaction/extrapolation curve
suppressMessages({  
  p3 <- ggiNEXT(iNEXT_data_Nin, type=3, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

suppressMessages({    
  suppressWarnings({  
    ggarrange(p1, p2, p3 + rremove("x.text"), 
          labels = c("A", "B", "C"),
          ncol = 2, nrow = 2, common.legend = T, legend = "right")
    }) 
  })

13 Philippines

iNEXT_data_Phi <- readRDS("iNEXT_data_Phi.rds")

palette <- c("#875f1f","#d39531","#d39531","#d39531","#875f1f","#d39531",
             "#fab039","#3b290d","#ad7a28","#614416","#614416","#875f1f",
             "gray34","#614416","#ad7a28","#3b290d","#fab039","#614416",
             "#ad7a28","#ad7a28","#875f1f","gray34")

# Sample-size-based rarefaction/extrapolation curve
suppressMessages({  
  p1 <- ggiNEXT(iNEXT_data_Phi, type=1, color.var = "Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

# Sample completeness curve
suppressMessages({  
  p2 <- ggiNEXT(iNEXT_data_Phi, type=2, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

# Coverage-based rarefaction/extrapolation curve
suppressMessages({  
  p3 <- ggiNEXT(iNEXT_data_Phi, type=3, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

suppressMessages({    
  suppressWarnings({  
    ggarrange(p1, p2, p3 + rremove("x.text"), 
          labels = c("A", "B", "C"),
          ncol = 2, nrow = 2, common.legend = T, legend = "right")
    }) 
  })

14 Scandola

iNEXT_data_Sca <- readRDS("iNEXT_data_Sca.rds")

palette <- c("#80341b","#a64423","gray34","#a64423","#f26333","#80341b",
             "#cc532b","#80341b","#80341b","#cc532b","#a64423","#33150b",
             "#f26333","#80341b","#f26333","#f26333","#a64423","#cc532b",
             "#cc532b","#592513","gray34")

# Sample-size-based rarefaction/extrapolation curve
suppressMessages({  
  p1 <- ggiNEXT(iNEXT_data_Sca, type=1, color.var = "Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

# Sample completeness curve
suppressMessages({  
  p2 <- ggiNEXT(iNEXT_data_Sca, type=2, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

# Coverage-based rarefaction/extrapolation curve
suppressMessages({  
  p3 <- ggiNEXT(iNEXT_data_Sca, type=3, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

suppressMessages({    
  suppressWarnings({  
    ggarrange(p1, p2, p3 + rremove("x.text"), 
          labels = c("A", "B", "C"),
          ncol = 2, nrow = 2, common.legend = T, legend = "right")
    }) 
  })

15 Seychellen

iNEXT_data_Sey <- readRDS("iNEXT_data_Sey.rds")

palette <- c("#d64259","#8a2b39","#8a2b39","gray34","#d64259","#fc4e68",
             "#b03749","#8a2b39","#b03749","#631f29","#631f29","#d64259",
             "#d64259","#631f29","#8a2b39","#631f29","#fc4e68","#fc4e68",
             "#b03749","gray34","#b03749","gray34")

# Sample-size-based rarefaction/extrapolation curve
suppressMessages({  
  p1 <- ggiNEXT(iNEXT_data_Sey, type=1, color.var = "Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

# Sample completeness curve
suppressMessages({  
  p2 <- ggiNEXT(iNEXT_data_Sey, type=2, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

# Coverage-based rarefaction/extrapolation curve
suppressMessages({  
  p3 <- ggiNEXT(iNEXT_data_Sey, type=3, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

suppressMessages({    
  suppressWarnings({  
    ggarrange(p1, p2, p3 + rremove("x.text"), 
          labels = c("A", "B", "C"),
          ncol = 2, nrow = 2, common.legend = T, legend = "right")
    }) 
  })

16 SharkBay

iNEXT_data_Sha <- readRDS("iNEXT_data_Sha.rds")

palette <- c("#bf7aac","#bf7aac","#996289","#734967","#bf7aac","#33202e",
             "#e693ce","#bf7aac","#e693ce","#33202e","#e693ce","gray34",
             "#734967","#bf7aac","#996289","#33202e","#734967","#996289",
             "#e693ce","#33202e","#734967","gray34")

# Sample-size-based rarefaction/extrapolation curve
suppressMessages({  
  p1 <- ggiNEXT(iNEXT_data_Sha, type=1, color.var = "Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

# Sample completeness curve
suppressMessages({  
  p2 <- ggiNEXT(iNEXT_data_Sha, type=2, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

# Coverage-based rarefaction/extrapolation curve
suppressMessages({  
  p3 <- ggiNEXT(iNEXT_data_Sha, type=3, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

suppressMessages({    
  suppressWarnings({  
    ggarrange(p1, p2, p3 + rremove("x.text"), 
          labels = c("A", "B", "C"),
          ncol = 2, nrow = 2, common.legend = T, legend = "right")
    }) 
  })

17 SouthAfrica

iNEXT_data_SoA <- readRDS("iNEXT_data_SoA.rds")

palette <- c("#2b3966","#607fe6","#607fe6","#3b4e8c","#4b63b3","#4b63b3",
             "#4b63b3","#5b78d9","#607fe6","#5b78d9","#5b78d9","#2b3966",
             "#2b3966","#2b3966","#3b4e8c","#5b78d9","#3b4e8c","#607fe6",
             "#4b63b3","#5b78d9","#3b4e8c","gray34")

# Sample-size-based rarefaction/extrapolation curve
suppressMessages({  
  p1 <- ggiNEXT(iNEXT_data_SoA, type=1, color.var = "Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

# Sample completeness curve
suppressMessages({  
  p2 <- ggiNEXT(iNEXT_data_SoA, type=2, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

# Coverage-based rarefaction/extrapolation curve
suppressMessages({  
  p3 <- ggiNEXT(iNEXT_data_SoA, type=3, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

suppressMessages({    
  suppressWarnings({  
    ggarrange(p1, p2, p3 + rremove("x.text"), 
          labels = c("A", "B", "C"),
          ncol = 2, nrow = 2, common.legend = T, legend = "right")
    }) 
  })

18 SouthernOcean

iNEXT_data_SoO <- readRDS("iNEXT_data_SoO.rds")

palette <- c("#52faf4","#20615f","#319491","#52faf4","#42c7c2","#319491",
             "#42c7c2","#0f2e2d","#319491","#0f2e2d","#20615f","gray34",
             "#20615f","#42c7c2","#52faf4","#20615f","#52faf4","#0f2e2d",
             "#0f2e2d","#319491","#42c7c2","#52faf4","#20615f","gray34",
             "gray34")

# Sample-size-based rarefaction/extrapolation curve
suppressMessages({  
  p1 <- ggiNEXT(iNEXT_data_SoO, type=1, color.var = "Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

# Sample completeness curve
suppressMessages({  
  p2 <- ggiNEXT(iNEXT_data_SoO, type=2, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

# Coverage-based rarefaction/extrapolation curve
suppressMessages({  
  p3 <- ggiNEXT(iNEXT_data_SoO, type=3, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

suppressMessages({    
  suppressWarnings({  
    ggarrange(p1, p2, p3 + rremove("x.text"), 
          labels = c("A", "B", "C"),
          ncol = 2, nrow = 2, common.legend = T, legend = "right")
    }) 
  })

19 Wadden

iNEXT_data_Wad <- readRDS("iNEXT_data_Wad.rds")

palette <- c("gray34","#50b34d","#50b34d","#2e662c","#2e662c","#2e662c",
             "#61d95d","gray34","#50b34d","#3f8c3c","#3f8c3c","#3f8c3c",
             "#3f8c3c","#73ff6e","gray34","#2e662c","#50b34d","#2e662c",
             "#61d95d","#61d95d","#73ff6e","#73ff6e","#61d95d","#73ff6e",
             "#50b34d","gray34","#73ff6e","#50b34d","#61d95d","#61d95d",
             "#61d95d","#2e662c","#50b34d","#50b34d","#61d95d","#73ff6e",
             "#73ff6e","#2e662c","gray34","#50b34d","#2e662c","#2e662c",
             "#73ff6e","gray34","gray34","gray34")

# Sample-size-based rarefaction/extrapolation curve
suppressMessages({  
  p1 <- ggiNEXT(iNEXT_data_Wad, type=1, color.var = "Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

# Sample completeness curve
suppressMessages({  
  p2 <- ggiNEXT(iNEXT_data_Wad, type=2, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

# Coverage-based rarefaction/extrapolation curve
suppressMessages({  
  p3 <- ggiNEXT(iNEXT_data_Wad, type=3, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

suppressMessages({    
  suppressWarnings({  
    ggarrange(p1, p2, p3 + rremove("x.text"), 
          labels = c("A", "B", "C"),
          ncol = 2, nrow = 2, common.legend = T, legend = "right")
    }) 
  })

20 Yemen

iNEXT_data_Yem <- readRDS("iNEXT_data_Yem.rds")

palette <- c("#030102","#ff66cc","#331429","#cc52a3","#ff66cc","#662952",
             "#993d7a","gray34")

# Sample-size-based rarefaction/extrapolation curve
suppressMessages({  
  p1 <- ggiNEXT(iNEXT_data_Yem, type=1, color.var = "Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

# Sample completeness curve
suppressMessages({  
  p2 <- ggiNEXT(iNEXT_data_Yem, type=2, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

# Coverage-based rarefaction/extrapolation curve
suppressMessages({  
  p3 <- ggiNEXT(iNEXT_data_Yem, type=3, color.var="Assemblage") +
  scale_colour_manual(values=palette) +
  scale_fill_manual(values=palette) 
  }) 

suppressMessages({    
  suppressWarnings({  
    ggarrange(p1, p2, p3 + rremove("x.text"), 
          labels = c("A", "B", "C"),
          ncol = 2, nrow = 2, common.legend = T, legend = "right")
    }) 
  })